Adobe Systems agreed to buy the maker of PhoneGap, a well-known platform for building HTML5 and Javascript apps that work on both Android and iOS devices. The deal comes at a time when Adobe’s Flash technology is gradually being phased out by many developers after Apple balked from supporting it on iOS devices.

At the same time, mobile developers face a fragmented market landscape in which they have to support multiple platforms and devices — a daunting challenge for smaller studios which have limited engineering resources.

PhoneGap’s maker Nitobi recently launched a premium, paid version of its service called PhoneGap Build last year, which has extra proprietary code for third-party developers and costs anywhere from $12 to $90 per month. This is the part that Adobe says will complement its other offerings in Flash development as more mobile developers migrate away from the technology to HTML5.

“PhoneGap makes it drop dead simple to develop native applications across devices using your existing HTML and JavaScript development skills,” wrote Kenneth Berger, Adobe’s senior product manager on mergers and acquisitions. “As mobile devices continue to fragment and more and more companies need mobile apps deployed across platforms, this problem will only become more important to solve.”

PhoneGap’s original code is being donated to the Apache Foundation where it will still be open-source under the name of CallBack. Nitobi says PhoneGap’s framework has been downloaded more than 600,000 times and it supports a number of apps like IGN’s game check-in app Dominate. We’re not aware of any high-profile gaming clients though as the bigger developers tend to focus on native apps with a more seamless user experience.

PhoneGap’s code will still be open source as it will be donated to the Apache Foundation under the name CallBack. After the acquisition presumably closes next month, Nitobi’s Vancouver-based team will join Adobe. Terms of the deal were not disclosed.